Two-step approach for occupancy estimation in intensive care units based on Bayesian optimization techniques

Due to the high occupational pressure suffered by intensive care units (ICUs), a correct estimation of the patients’ length of stay (LoS) in the ICU is of great interest to predict possible situations of collapse, to help healthcare personnel to select appropriate treatment options and to predict patients’ conditions. There has been a high amount of data collected by biomedical sensors during the continuous monitoring process of patients in the ICU, so the use of artificial intelligence techniques in automatic LoS estimation would improve patients’ care and facilitate the work of healthcare personnel. In this work, a novel methodology to estimate the LoS using data of the first 24 h in the ICU is presented. To achieve this, XGBoost, one of the most popular and efficient state-of-the-art algorithms, is used as an estimator model, and its performance is optimized both from computational and precision viewpoints using Bayesian techniques. For this optimization, a novel two-step approach is presented. The methodology was carefully designed to execute codes on a high-performance computing system based on graphics processing units, which considerably reduces the execution time. The algorithm scalability is analyzed. With the proposed methodology, the best set of XGBoost hyperparameters are identified, estimating LoS with a MAE of 2.529 days, improving the results reported in the current state of the art and probing the validity and utility of the proposed approach.Agencia Gallega de Innovación | Ref. IN845D-2020/29Agencia Gallega de Innovación | Ref. IN607B-2021/1

Guidelines for Linked Data generation and publication: an example in building energy consumption

Linked Data is the key paradigm of the Semantic Web, a new generation of the World Wide Web that promises to bring meaning (semantics) to data. A large number of both public and private organizations have published their data following the Linked Data principles, or have done so with data from other organizations. To this extent, since the generation and publication of Linked Data are intensive engineering processes that require high attention in order to achieve high quality, and since experience has shown that existing general guidelines are not always sufficient to be applied to every domain, this paper presents a set of guidelines for generating and publishing Linked Data in the context of energy consumption in buildings (one aspect of Building Information Models). These guidelines offer a comprehensive description of the tasks to perform, including a list of steps, tools that help in achieving the task, various alternatives for performing the task, and best practices and recommendations. Furthermore, this paper presents a complete example on the generation and publication of Linked Data about energy consumption in buildings, following the presented guidelines, in which the energy consumption data of council sites (e.g., buildings and lights) belonging to the Leeds City Council jurisdiction have been generated and published as Linked Data

Effectiveness of the 23-valent polysaccharide pneumococcal vaccine against invasive pneumococcal disease in people 60 years or older

<p>Abstract</p> <p>Background</p> <p>The 23-valent polysaccharide pneumococcal vaccine (PPV) is currently recommended in elderly and high-risk adults. However, its efficacy in preventing pneumococcal infections remains controversial. This study assessed the clinical effectiveness of vaccination against invasive pneumococcal disease (IPD) among people over 60 years.</p> <p>Methods</p> <p>Population-based case-control study that included 88 case patients over 60 years-old with a laboratory-confirmed IPD (bacteraemic pneumonia, meningitis or sepsis) and 176 outpatient control subjects who were matched by primary care centre, age, sex and risk stratum. Adjusted odds ratios (ORs) for vaccination were calculated using conditional logistic regression, controlling for underlying conditions. Vaccine effectiveness was estimated as (1 - OR) ×100.</p> <p>Results</p> <p>Pneumococcal vaccination rate was significantly lower in cases than in control subjects (38.6% <it>vs </it>59.1%; p = 0.002). The adjusted vaccine effectiveness was 72% (OR: 0.28; 95% CI: 0.15-0.54) against all IPD and 77% (OR: 0.23; 95% CI: 0.08-0.60) against vaccine-type IPD. Vaccination was significantly effective against all IPD in both age groups: 60-79 years-old (OR 0.32; 95% CI: 0.14-0.74) and people 80 years or older (OR: 0.29; 95% CI: 0.09-0.91). Vaccination appears significantly effective as for high-risk immunocompetent subjects (OR: 0.29; 95% CI: 0.11-0.79) as well as for immunocompromised subjects (OR: 0.12; 95% CI: 0.03-0.53).</p> <p>Conclusion</p> <p>These findings confirm the effectiveness of the 23-valent PPV against IPD, and they also support the benefit of vaccination in preventing invasive infections among high-risk and older people.</p

Hepatitis B Virus Variants with Multiple Insertions and/or Deletions in the X Open Reading Frame 3 ' End: Common Members of Viral Quasispecies in Chronic Hepatitis B Patients

Hepatitis B virus; Insertions; Next-generation sequencingVirus de l'hepatitis B; Insercions; Seqüenciació de nova generacióVirus de la hepatitis B; Inserciones; Secuenciación de próxima generaciónDeletions in the 3′ end region of the hepatitis B virus (HBV) X open reading frame (HBX) may affect the core promoter (Cp) and have been frequently associated with hepatocellular carcinoma (HCC). The aim of this study was to investigate the presence of variants with deletions and/or insertions (Indels) in this region in the quasispecies of 50 chronic hepatitis B (CHB) patients without HCC. We identified 103 different Indels in 47 (94%) patients, in a median of 3.4% of their reads (IQR, 1.3–8.4%), and 25% (IQR, 13.1–40.7%) of unique sequences identified in each quasispecies (haplotypes). Of those Indels, 101 (98.1%) caused 44 different altered stop codons, the most commonly observed were at positions 128, 129, 135, and 362 (putative position). Moreover, 39 (37.9%) Indels altered the TATA-like box (TA) sequences of Cp; the most commonly observed caused TA2 + TA3 fusion, creating a new putative canonical TATA box. Four (8%) patients developed negative clinical outcomes after a median follow-up of 9.4 (8.7–12) years. In conclusion, we observed variants with Indels in the HBX 3′ end in the vast majority of our CHB patients, some of them encoding alternative versions of HBx with potential functional roles, and/or alterations in the regulation of transcription.This research was funded by Instituto de Salud Carlos III and co-financed by the European Regional Development Fund (ERDF), grant number PI18/01436; PI19/00301; and by the Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business, grant number IDI-20200297. The APC was funded by the grant PI18/01436

Standardization of electroencephalography for multi-site, multi-platform and multi-investigator studies: Insights from the canadian biomarker integration network in depression

Subsequent to global initiatives in mapping the human brain and investigations of neurobiological markers for brain disorders, the number of multi-site studies involving the collection and sharing of large volumes of brain data, including electroencephalography (EEG), has been increasing. Among the complexities of conducting multi-site studies and increasing the shelf life of biological data beyond the original study are timely standardization and documentation of relevant study parameters. We presentthe insights gained and guidelines established within the EEG working group of the Canadian Biomarker Integration Network in Depression (CAN-BIND). CAN-BIND is a multi-site, multi-investigator, and multiproject network supported by the Ontario Brain Institute with access to Brain-CODE, an informatics platform that hosts a multitude of biological data across a growing list of brain pathologies. We describe our approaches and insights on documenting and standardizing parameters across the study design, data collection, monitoring, analysis, integration, knowledge-translation, and data archiving phases of CAN-BIND projects. We introduce a custom-built EEG toolbox to track data preprocessing with open-access for the scientific community. We also evaluate the impact of variation in equipment setup on the accuracy of acquired data. Collectively, this work is intended to inspire establishing comprehensive and standardized guidelines for multi-site studies

Standardized Hepatitis B Virus RNA Quantification in Untreated and Treated Chronic Patients: a Promising Marker of Infection Follow-Up.

The measurement and interpretation of HBV DNA and RNA levels in HBV infected patients treated with antiviral therapy supports the objective of HBV disease management. Here, we quantified circulating HBV RNA through a standardized and sensitive assay in follow-up samples from both naive and treated patients as a marker of infection evolution. HBV DNA (HBV DNA for use in Cobas 6800/8800 Automated Roche Molecular Systems), RNA (Roche HBV RNA Investigational Assay for use in the Cobas 6800/8800; Roche), HBeAg and HBsAg (Elycsys HBsAg chemiluminescence immunoassay by Cobas 8000; Roche), and core-related antigen (Lumipulse G chemiluminescence assay; Fujirebio) levels were measured in cohorts of untreated or nucleos(t)ide treated, HBV-infected subjects in an outpatient hospital setting. HBV DNA levels in untreated people were 3.6 log10 higher than corresponding RNA levels and were stable over 5 years of observation. While only five of 52 treated patients had DNA levels below the lower limit of quantification (10 IU/mL) at the end of follow-up, 13 had HBV RNA levels persistently above this limit, including eight with undetectable DNA. In samples with undetectable core-related antigen we observed a median HBsAg titer 2.7-fold higher than in samples with undetectable RNA (adjusted P = 0.012). Detectable HBV RNA with undetectable HBV DNA was a negative predictor of HBsAg decrease to a level ≤100 IU/mL (P = 0.03). In naive patients the difference between HBV DNA and RNA was higher than previously reported. HBV RNA rapidly decreased during treatment. However, in some cases, it was detectable even after years of effective therapy, being a negative predictor of HBsAg decrease. The investigational RNA assay for use on the Cobas 6800/8800 instruments is a sensitive and standardized method that could be applied in general management of HBV infection. IMPORTANCE This study focused on the quantification of circulating HBV RNA by using a standardized and sensitive assay. Thanks to this system we observed a higher difference between circulating HBV DNA and RNA than previously reported. In treated patients, HBV RNA decreased together with DNA, although some patients presented detectable levels even after years of successful antiviral treatment, suggesting a persistent viral transcription. Of note, the detection of viral RNA when HBV DNA is undetectable was a negative predictor of HBsAg decrease to a level ≤100 IU/mL. This assay could be extremely helpful in HBV patients management to study viral transcription and to identify those treated patients that may achieve sustained viral suppression

Efficient and reliable nonlocal damage models

We present an efficient and reliable approach for the numerical modelling of failure with nonlocal damage models. The two major numerical challenges––the strongly nonlinear, highly localized and parameter-dependent structural response of quasi-brittle materials, and the interaction between nonadjacent finite elements associated to nonlocality––are addressed in detail. Reliability of the numerical results is ensured by an h-adaptive strategy based on error estimation. We use a residual-type error estimator for nonlinear FE analysis based on local computations, which, at the same time, accounts for the nonlocality of the damage model. Efficiency is achieved by a proper combination of load-stepping control technique and iterative solver for the nonlinear equilibrium equations. A major issue is the computation of the consistent tangent matrix, which is nontrivial due to nonlocal interaction between Gauss points. With computational efficiency in mind, we also present a new nonlocal damage model based on the nonlocal average of displacements. For this new model, the consistent tangent matrix is considerably simpler to compute than for current models. The various ideas discussed in the paper are illustrated by means of three application examples: the uniaxial tension test, the three-point bending test and the single-edge notched beam test.Peer ReviewedPostprint (author’s final draft

High thyrotropin is critical for cardiac electrical remodeling and arrhythmia vulnerability in hypothyroidism

Background: Hypothyroidism, the most common endocrine disease, induces cardiac electrical remodeling that creates a substrate for ventricular arrhythmias. Recent studies report that high thyrotropin (TSH) levels are related to cardiac electrical abnormalities and increased mortality rates. The aim of the present work was to investigate the direct effects of TSH on the heart and its possible causative role in the increased incidence of arrhythmia in hypothyroidism. Methods: A new rat model of central hypothyroidism (low TSH levels) was created and characterized together with the classical propylthiouracil-induced primary hypothyroidism model (high TSH levels). Electrocardiograms were recorded in vivo, and ionic currents were recorded from isolated ventricular myocytes in vitro by the patch-clamp technique. Protein and mRNA were measured by Western blot and quantitative reverse transcription polymerase chain reaction in rat and human cardiac myocytes. Adult human action potentials were simulated in silico to incorporate the experimentally observed changes. Results: Both primary and central hypothyroidism models increased the L-type Ca2+ current (ICa-L) and decreased the ultra-rapid delayed rectifier K+ current (IKur) densities. However, only primary but not central hypothyroidism showed electrocardiographic repolarization abnormalities and increased ventricular arrhythmia incidence during caffeine/dobutamine challenge. These changes were paralleled by a decrease in the density of the transient outward K+ current (Ito) in cardiomyocytes from animals with primary but not central hypothyroidism. In vitro treatment with TSH for 24 hours enhanced isoproterenol-induced spontaneous activity in control ventricular cells and diminished Ito density in cardiomyocytes from control and central but not primary hypothyroidism animals. In human myocytes, TSH decreased the expression of KCND3 and KCNQ1, Ito, and the delayed rectifier K+ current (IKs) encoding proteins in a protein kinase A–dependent way. Transposing the changes produced by hypothyroidism and TSH to a computer model of human ventricular action potential resulted in enhanced occurrence of early afterdepolarizations and arrhythmia mostly in primary hypothyroidism, especially under b-adrenergic stimulation. Conclusions: The results suggest that suppression of repolarizing K+ currents by TSH underlies most of the electrical remodeling observed in hypothyroidism. This work demonstrates that the activation of the TSHreceptor/protein kinase A pathway in the heart is responsible for the cardiac electrical remodeling and arrhythmia generation seen in hypothyroidism.Fil: Fernandez Ruocco, Maria Julieta. Universidade Federal do Rio de Janeiro; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani". Universidad Nacional de La Plata. Facultad de Ciencias Médicas. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani"; ArgentinaFil: Gallego, Monica. Universidad del País Vasco; EspañaFil: Rodriguez de Yurre, Ainhoa. Universidade Federal do Rio de Janeiro; Brasil. Universidad del País Vasco; EspañaFil: Zayas Arrabal, Julian. Universidad del País Vasco; EspañaFil: Echeazarra, Leyre. Universidade Federal do Rio de Janeiro; BrasilFil: Alquiza, Amaia. Universidad del País Vasco; EspañaFil: Fernández López, Victor. Universidad del País Vasco; EspañaFil: Rodriguez Robledo, Juan M.. Universidad del País Vasco; EspañaFil: Brito, Oscar. Instituto Nacional de Cardiologia; BrasilFil: Schleier, Ygor. Universidade Federal do Rio de Janeiro; BrasilFil: Sepúlveda, Marisa Noemí. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani". Universidad Nacional de La Plata. Facultad de Ciencias Médicas. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani"; ArgentinaFil: Oshiyama, Natalia F.. University of Campinas. Center for Biomedical Engineering; BrasilFil: Vila Petroff, Martin Gerarde. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani". Universidad Nacional de La Plata. Facultad de Ciencias Médicas. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani"; ArgentinaFil: Bassani, Rosana A.. University of Campinas. Center for Biomedical Engineering; BrasilFil: Medei, Emiliano H.. Universidade Federal do Rio de Janeiro; BrasilFil: Casis, Oscar. Universidad del País Vasco; Españ

Biofilm formation at the solid-liquid and air-liquid interfaces by Acinetobacter species

Abstract Background: The members of the genus Acinetobacter are Gram-negative cocobacilli that are frequently found in the environment but also in the hospital setting where they have been associated with outbreaks of nosocomial infections. Among them, Acinetobacter baumannii has emerged as the most common pathogenic species involved in hospital-acquired infections. One reason for this emergence may be its persistence in the hospital wards, in particular in the intensive care unit; this persistence could be partially explained by the capacity of these microorganisms to form biofilm. Therefore, our main objective was to study the prevalence of the two main types of biofilm formed by the most relevant Acinetobacter species, comparing biofilm formation between the different species. Findings: Biofilm formation at the air-liquid and solid-liquid interfaces was investigated in different Acinetobacter spp. and it appeared to be generally more important at 25°C than at 37°C. The biofilm formation at the solid-liquid interface by the members of the ACB-complex was at least 3 times higher than the other species (80-91% versus 5-24%). In addition, only the isolates belonging to this complex were able to form biofilm at the air-liquid interface; between 9% and 36% of the tested isolates formed this type of pellicle. Finally, within the ACB-complex, the biofilm formed at the air-liquid interface was almost 4 times higher for A. baumannii and Acinetobacter G13TU than for Acinetobacter G3 (36%, 27% & 9% respectively). Conclusions: Overall, this study has shown the capacity of the Acinetobacter spp to form two different types of biofilm: solid-liquid and air-liquid interfaces. This ability was generally higher at 25°C which might contribute to their persistence in the inanimate hospital environment. Our work has also demonstrated for the first time the ability of the members of the ACB-complex to form biofilm at the air-liquid interface, a feature that was not observed in other Acinetobacter species